The Choice
by DecendentofGallifrey
Summary: Jodie Shepard has finally activated the Crucible, but there is still one last choice to be made. Warning Cannon Character Deaths. I do not own Mass Effect or any of its characters. Spoilers. If you have not played through Mass Effect 3 or the Mass Effect series and do not wish to know the ending do not read this.
1. Chapter 1

Everything hurt. Jodie Shepard felt as if she were holding the weight of the universe on her shoulders. She was fully aware of how heavy her body could be as she knelt. Shepard had done so much to get to this point.

"Wake up." The voice was childlike. Shepard slowly pulled herself onto her feet, swaying as pain tore through her body. She, as always, studiously ignored it. Lights were racing before her. Like the Prothean VI the lights resolved themselves into the shape of a child. A familiar child.

"What?" Shepard asked her eyes darting around the strange room before her. The war against the Reapers raged outside yet no sound found her. An Alliance ship was shred to pieces as a Reaper's beam flashed an angry red. Her thoughts darted to Joker. Let them be okay. "Where am I?" She asked. What had she been doing before this? Her thoughts and memories were blurry and filled with death and pain. There was a voice…someone important telling her that their last resort….their plan wasn't working. The Crucible wasn't working. Another ship was destroyed. They were all going to die.

And it was all her fault.

"The Citadel. It's my home." The child-like figure stated. She knew this child, it was the same who had haunted her dreams. White jacket and innocent eyes she could see him as clearly as she could in her dreams. Always running with the whispers of the dead in her ears chasing after the child as Reapers bore down upon them both.

"Who are you?"

"I am the Catalyst." The child replied simply. Shepard stared at him for a few moments in shock. The room beyond the child loomed ominous and strangely silent. It seemed as if the room was waiting on something. Three paths split a ways from where she stood.

"I thought the Citadel was the Catalyst." Shepard said confused.

"No," the child said forcefully, "the Citadel is part of me."

"I need to stop the Reapers." Shepard said feeling a bit desperate. Everyone was dying. And everyone who was fighting out there, every ship that got blown apart by Reapers, they were all there because she recruited them. "Do you know how I can do that?" Her voice was shaking. So much death.

"Perhaps." The child said. "I control the Reapers. They are my solution." The child turned away and began to walk towards the three branching paths. Feeling there was nothing else for her to do she limped after the child. Shepard knew that looks could be deceiving, hell, Liara looked like the sweetest person and she was the Shadow Broker. This child-like thing could be the cause of all of this destruction, but the thought still made her stomach twist in an unpleasant way. She gripped her middle as she stumbled a few more steps.

"The solution to what?" She asked stopping. The child walked a few steps before realizing she had stopped.

"Chaos." The Catalyst said over its shoulder continuing to walk away. Shepard gathered her strength and began to limp after the child once more. As if the child could sense her following he continued with his answer. "The created will always rebel against their creators." The Geth and the Quarians flashed across her vision. Tali watching in anguish as her race burned before her eyes. Tali taking off her mask seconds before she let herself fall backwards over the cliff. Shepard tried to forget the sound her body made as it hit the rocks below. "But we found a way to stop that from happening. A way to restore order."

"By wiping out organic life?" Shepard asked anger underlying her words. She stopped once more and this time the child stopped as well.

"No." The Catalyst turned to face her seeming resolute. "We harvest advanced civilizations leaving the younger ones alone." She couldn't help the look of anger that crossed her face. As if that made up for the decimation of so many countless civilizations. The child had already turned away and began to walk again. "Just as we left your people alive the last time we were here." The Catalyst added.

"But you killed the rest."

"We helped them ascend so they could make way for new life, storing the old life in Reaper form." The Catalyst stopped once more turning to watch a Reaper pass by. So many little ships swirled and danced about it as they fought for their existence.

"I think we'd rather keep our own form."

The Catalyst looked to Shepard. "No, you can't. Without us to stop it synthetics would destroy all organics. We've created this cycle so that never happens. That's the solution."

"You said you're the Catalyst but…what are you?"

"A construct. An intelligence designed eons ago to solve a problem. I was created to bring balance, to be the Catalyst of peace between synthetics and organics."

"So you're just an AI." Shepard breathed.

"In as much as you are just an animal. I embody the collective intelligence of all Reapers." The Catalyst said looking up at Shepard. She was right. Looks could be deceiving.

"But you were created…" She stated slowly.

"Correct."

"By who?" Shepard pressed.

"By ones who recognized that conflict would always arise between synthetics and organics. I was first created to oversee the relations between synthetic and organic life; to establish a connection. But our efforts always ended in conflict so a new solution was required."

"The Reapers?" Shepard asked horrified.

"Precisely." The Catalyst answered.

"Where did the Reapers come from? Did you create them?" She asked curiosity getting the better of her.

"My creators gave them form, I gave them function. They, in turn, give me purpose." The Catalyst explained. "The Reapers are a synthetic representation of my creators."

"…Leviathans." Shepard said in understanding.

"Yes. They created me to oversee their relations with synthetic and organic life to establish a connection. They became the first true Reaper. They did not approve but it was the only solution."

Shepard frowned. "You've said that before. But how do the Reapers solve anything?"

"Organics create synthetics to improve their own existence," the Catalyst explained, "but those improvements have limits. To exceed those limits synthetics must be allowed to evolve. They must, by definition, surpass their creators. The result is conflict, destruction, chaos. It is inevitable." The Catalyst sounded so sure, but Shepard had seen opposite. Yes the Geth destroyed the Quarians, but only because they refused to back down. The Geth were helping them now working with, instead of against, organic life. "Reapers harvest all life- organic and synthetic- preserving them before they are forever lost to this conflict."

Shepard could not believe what she was hearing. How could this child, the Catalyst, think that this was not conflict? "We're at war with the Reapers right now!" She said tensely.

"You may be in conflict with the Reapers but they are not interested in war."

Shepard let out a small harsh laugh. "I find that hard to believe."

The Catalyst glanced to the large beam of energy that ran through the middle path. "When fire burns is it at war? Is it in conflict? Or is it simply doing what it was created to do? We are no different." The Catalyst said resolutely. "We harvest your bodies, your knowledge, your creations. We preserve it to be born in the form of a new Reaper. Like a cleansing fire we restore balance. New life both organic and synthetic can once again flourish."

Shepard realized that she was getting nowhere fast with this strain of conversation, and the more time she wasted the more people died fighting against his "solution".

"I met your creators. They told me what you did to them." The accusation in her voice was palpable.

"We did as we were expected."

Shepard continued on. "They said you betrayed them. That you turned them into Harbinger."

"When they asked that I solved the problem of conflict they failed to understand they were part of the problem themselves." The Catalyst said moving slightly so that he almost looked as if he were pacing for a moment. "The flaws of their organic reasoning could not perceive this. They lacked to foresight to understand that their destruction was part of the very solution they required."

Shepard felt horrified. "Well," She said, "they've joined this war now."

"And I welcome their involvement. I am only facilitating their request." The Catalyst said calmly.

Outside more people were dying. Shepard almost wished that she could hear the explosions that were taking place. She knew that it was impossible, but she still wished that she could. To see people dying and explosions happening around her and to hear or physically feel nothing was disturbing on multiple levels.

"What do you know about the Crucible?" Shepard asked wanting nothing more than to lay down. The pain was slowly getting to her.

"The device you refer to as the Crucible is little more than a power source. However, in combination with the Citadel and the Relays it is capable of releasing tremendous amounts of energy throughout the galaxy. It's crude but effective and adaptive in its design."

"Who designed it?"

"You would not know them and there is not enough time to explain." The Catalyst still spoke with an infuriating calm. He was so different from EDI in this moment. "We first noted the concept for this device several cycles ago. With each passing cycle the design has no doubt evolved."

"Why didn't you stop it?"

"We believed the concept had been eradicated. Clearly organics are more resourceful than we realized." He sounded almost impressed…almost.

The Catalyst would never understand, Shepard decided, but she would still try to convey the horror that it had caused. "But you're taking away our future. Without our future we have no hope. Without hope," Shepard continued her voice gaining volume and confidence, "we might as well be machines. Programed to do what we're told."

"You have hope." Shepard frowned in confusion. "More than you think." The Catalyst added. "The fact that you are standing here, the first organic ever, proves it. But it also proves my solution won't work anymore."

"So now what?" She was exhausted and that fact was now showing in her voice.

"We find a new solution."

Shepard looked around the room once more a foreboding feeling coming over her. "Why are you telling me this? Why help me?"

"You have altered the variables."

It was painful to breathe at this point. Shepard's breaths stuttered a small bit before she looked back to the child. "What do you mean?"

"The Crucible changed me, created new," The Catalyst paused for a moment in thought, "possibilities. But I can't make them happen. If there is to be a new solution, you must act." Shepard froze. It was up to her…to do what though? "It is now in your power to destroy us." The Catalyst said pointing to the right most branch. The pathway was bathed in red light and at the end was a small tube. Shepard guessed that she would have to shoot the tube in order to destroy the Reapers.

She could almost see Anderson walking towards the tube, gun in hand, destroying the Reaper threat once and for all. Anderson would want her to do it. Her mind grazed over the last time she saw him. They sat, waiting for the Crucible to do its job, earth spread beneath them like a sapphire and emerald jewel.

"_Commander." Anderson said as Shepard sat beside him. The illusive man was dead, and the war was finally going to be over. They both sat bloody and broken staring towards Earth, towards home. _

"_We did it." Shepard said in relief. All of the fights, all of the deaths, and fear had finally led to this. They were going to defeat the Reapers…they were going to save everyone._

"_Yes we did." Anderson said after a moment. He sounded just as relieved as Shepard. "It's quite a view." He said looking over the Earth with fondness. Shepard looked beyond the debris of the war raging outside to look at her home. She had been born there…raised an orphan. Everything changed when she joined the Alliance. Who could have believed that the little orphan girl was now saving that majestic cloud wreathed planet. Hell, she helped save the universe. _

_Shepard's breathing was unsteady as she replied. "Best seats in the house." _

"_You ever wonder how things would have been different? How our lives would be different if this hadn't happened?" Anderson asked. _

"_Sure." Shepard replied. And she had. She would have never met her friends, her love. _

"_I never had a family, Shepard." Anderson spoke softly. "Never had children."_

"_They'll be time enough for that now." Shepard spoke through broken breaths. _

_Anderson began to laugh which quickly shifted to coughing then back to laughter. "I think that ship has sailed. What about you? Ever think about settling down?"_

_Without meaning to Shepard got a glimpse of Garrus' face. She thought about her life. "I'm a soldier, Anderson. Like you. Not really fit for doing anything else."_

"_I don't know, Shepard." Anderson said. "I think you'd make a great mother."_

"_Uh huh." Shepard said amused. There was a few seconds of silence between the two. _

"_Think how proud your kids would be." Anderson continued his face softening. "Telling everyone their…their mom is Commander Shepard." Anderson seemed like he couldn't quite catch his breath._

"_I don't know about that. Not everything I've done is something to be proud of." This time it was Tali's face that flashed before her eyes._

"_God," Anderson breathed, "feels like years since I…just sat down." _

"_I think you earned a rest." Shepard told him. He made a small sound of agreement. And then his eyes began to roll back. "Stay with me." Shepard said feeling slightly panicked. "We're almost through this."_

"_You did good, child." Anderson told her. "You did good." He began to sag underneath his own weight. "I'm proud of you." He let his head drop his body relaxing._

"_Thank you, sir." Shepard replied glancing towards him. He wasn't moving. "Anderson?" Shepard asked sorrow beginning to mount. Anderson did not reply. Shepard was too exhausted for tears. Instead she looked back to her planet Anderson's final words ringing in her ears._


	2. Chapter 2

"But be warned," The Catalyst suddenly spoke shattering the memory of Anderson's final moments, "others will be destroyed as well. The Crucible will not discriminate. All synthetics will be targeted." Shepard felt a sudden flash of panic. The Geth. "Even you are partly synthetic." The Catalyst reminded her.

"What exactly will happen?" Shepard asked.

The Catalyst shifted his stance and looked up at the great machine before them. "Your Crucible device appears to be largely intact, however, the effects of the blast will not be constrained to the Reapers. Technology you rely on will be affected, but those who survive should have little difficulty repairing the damage."

"There will still be losses." The Catalyst continued. "But no more than what has already been lost."

"But the Reapers will be destroyed?" Shepard asked her mind on Anderson.

"Yes, but the peace won't last." Shepard frowned when he said this. "Soon your children will create synthetics and the chaos will come back."

Shepard considered this option, but couldn't bring herself to do it. Anderson said he was proud of her, but she didn't always do what he thought was right. She couldn't destroy all synthetics…she couldn't murder and entire race of sentient beings just because they weren't organic. She couldn't destroy EDI. That would make her no better than the reapers themselves.

"There has to be another way." Shepard said almost desperately.

"There is." The Catalyst confirmed. "You could instead use the energy of the Crucible to seize control of the Reapers." The Catalyst pointed to the left most path. It was bathed in a blue light and had four prongs that she guessed a person would grab in order to take control. It was all too easy to see the illusive man taking control. He had raved about it for so long.

"So the illusive man was right after all." Shepard sighed.

"Yes, but he could have never taken control…because we already controlled him." Shepard understood that much. Anderson and Shepard could see the indoctrination clearly on the leader of Cerberus.

"But I can."

"You will die." The Catalyst warned. "You will control us, but you will lose everything you have."

Shepard narrowed her eyes at the Catalyst. "How can I control the Reapers if I'm dead?"

The Catalyst turned towards her once more. "Your corporeal form will be dissolved, but your thoughts and even your memories will continue." Shepard slowly turned to look at the blue bathed path. "Your connection to your kind will be lost though you will remain aware of their existence."

"But the Reapers will obey me?"

"Yes." The Catalyst said. "We will be yours to control and direct as you see fit."

Shepard considered this option. She could save everyone…and no one would die. Well…no one but her. But it sounded so much like indoctrination….and there was always the threat that it wouldn't work. She felt in her stomach that it would though. It would work and they would be safe. But if she lost her connection to humanity….to organics….how could she guarantee that she would not end up like the Catalyst. Caring only about the solution…

"There is another solution." The Catalyst spoke. Shepard looked to him sharply. "Synthesis." He said pointing to the beam directly ahead of her. The energy sparked and shifted before her.

"And that is?" Shepard asked glancing to the Catalyst.

"Add your energy to the Crucibles. The chain reaction will combine all synthetic and organic life into a new framework. A new DNA." The Catalyst said calm as ever.

"Explain how my energy can be added to the crucible." Shepard demanded.

"Your organic energy the essence of who and what you are will be broken down and then dispersed."

"To do what exactly?" Shepard had grown tired of the calm and matter of fact demeanor of the Catalyst. She briefly wondered if she could simply shoot him, but decided that it was a stupid idea and quickly discarded it.

"The energy of the Crucible released in this way will alter the matrix of all organic life in the galaxy. Organics seek perfection through technology, synthetics seek perfection through understanding. Organics will be perfected by integrating fully with synthetic technology. Synthetics, in turn, will finally have full understanding of organics. It is the ideal solution. Now that we know it is possible it is inevitable we will reach synthesis."

"Why couldn't you do it sooner?" Shepard asked suspicious.

"We have tried a similar solution in the past. But it has always failed."

Shepard was angry by this point. "Why?" She asked forcefully.

"Because the organics were not ready. It is not something that can be…forced." Shepard instantly wondered how many times they had tried to "force" this solution on organics. "You are ready and you may choose it." The Catalyst said simply.

"I don't know." Shepard said slowly.

"Why not? Synthetics are already a part of you. Can you imagine your life without them?" Synthetics were the only reason that she was alive right now. Without them she would be dead and this even might not have happened in the first place.

"And there will be peace?"

"The cycle will end. The Reapers will cease their harvest and the civilizations preserved in their forms will be connected to all of us." Almost like what the Asari do, thought Shepard. They bring in other races and cultures to make themselves stronger. "Synthesis is the final evolution of all life." The Catalyst said almost reverently.

"The paths are open. But you have to choose." The Catalyst took a small step back and watched impassively as Shepard stood there contemplating her decision.


	3. Chapter 3

Shepard wondered how the Catalyst knew that she was ready, but it was right. Shepard was ready to end this, she could go through with it even if it meant that she would die in the process. Her whole life had been leading towards this decision, and she already knew that the choice had been made. How could she choose anything else?

There was a strange sound and little ramps rose to connect to the main platform finishing the paths. Shepard slowly limped forwards, her heartbeat playing like a drum in her head. Each step brought her closer to the three choices…the one choice…that was going to change the fate of the universe. A universe she would never see.

She paused slightly when she came to the intersection of the three choices. Shepard briefly wondered if Anderson would be proud of her now. She stepped forwards, towards the large beam of energy that ran through the middle of the Crucible. Shepard wondered if she had the strength to even make it to the beam of energy.

Shepard let her mind drift as she moved one painful step at a time towards the beam of light. Towards Synthesis.

"_And the last time I had a briefing with Anderson, he told me to take care of you. The guy leading the resistance - on EARTH! - is worried about you! And I'm supposed to help!" Joker's eyes flashed with an intense protectiveness that Shepard had not seen before this moment. Any anger over thoughtless comments he had made were wiped away. _

"_I appreciate the thought, Joker. But I'm fine!" Shepard instantly assured him._

"_The hell you are!" Joker snapped._

The memory left Shepard thinking about her own body as she dragged it with sheer force of will towards the beam of light. The world had slowly shrank to the sight of the twisting energy. Joker would understand what she was about to do.

"_It's been an honor, Commander."_ Joker's voice felt so present, the memory so real that Shepard stopped for a second. Around her the war with the Reapers raged on.

"_Same here," Shepard had replied to Joker, "I don't know how this is going to end, but whatever happens…"_

"_What do you mean 'whatever happens'? Everyone knows what's going to happen." Joker said cutting her off. "You're going to kick some Reaper ass…that's what you're going to do." Joker had lifted himself up and turned to look Shepard in the eyes. He turned back to his controls a look of determination. "And I'll be flying you there in style."_

Shepard wondered if Joker was still flying around out there. She wondered if EDI was beside him. She began to walk again but the memories of her companions began to pour in.

"_Are you saying that submission is preferable to extinction?" Shepard asked EDI._

"_My primary function is to preserve and defend the…" EDI suddenly paused. "No." Her voice was strong, and it sounded remarkably…human. "No, I disagree." EDI continued her face settling into a look of determination. "Shepard, I am going to modify my self-preservation code now." _

"_Why?" Shepard asked._

"_Because the Reapers are repulsive. They are devoted to nothing but self-preservation." EDI explained. "I am different." EDI turned and glanced to the ground in thought. "When I think of Jeff, I think of the person who put his life in peril and freed me from a state of servitude. I would risk non-functionality for him. And my core programing should reflect that." _

_Shepard couldn't help the smile that bloomed over her face. "Sounds like you found a little humanity, EDI. Is it worth defending?"_

_EDI looked up from the floor and met Shepard's eyes resolutely. "To the death." She replied._

EDI was right of course…humanity was worth defending to the death. But so was she. So was Legion. Hell all of her crew. Shepard had met so many amazing people. So many of them willing to risk everything to save the universe. So many people had banded together to fight off the Reaper threat. The evidence of it was above and around her. So many people fighting them. And she could stop it…right now. Shepard's steps began to quicken and lengthen. Countless voices were ringing in her head.

"_Would have liked to run tests on seashells." _Mordin's voice was suddenly there as Shepard pushed herself forwards. _"Had to be me. Someone else might have gotten it wrong."_

"_I'm sorry."_ Tali's voice shivered through the air.

The Beam was beginning to loom in front of Shepard. The end of her life…for the lives of everyone who's left. It was a fair trade, she thought. She just hoped that whatever came after this…if there was anything after this…she hoped that she would be forgiven for all she had done to get here.

"_Kalahira, this one's heart is pure but beset by wickedness and contention." _Koylat's voice swirled around her, and Shepard swore that the pain in her body began to lessen. Shepard threw aside her gun and pushed herself into a run. She didn't need that gun anymore…the hard part was over.

"_Guide this one to where the traveler never tires, a lover never leaves, the hungry never starve." _It was her own voice this time. Soft and sad, filled with mourning. _"Guide this one, Kalahira, and she will be a companion to you as she was to me." _

"_Koylat," _Shepard's own voice was hushed in her own ears, "_why did the last verse say she?"_

"_The prayer was not for him, Commander. He has already asked forgiveness for the lives that he has taken." _Shepard pushed even harder as the end of the ledge began to approach. _"His wish was for you."_

"_Goodbye Thane…you won't be alone long." _Her voice said. The edge was right there. Shepard took a deep breath, her body coiling beneath her.

"_James told me," _A new voice began, "_there's an old saying here on earth." _Garrus….her Garrus. God she loved him. His voice was like a balm…lifting a weight she didn't realize she was carrying, but now that it was gone she could almost float with relief. Shepard had reached the end of the walkway. There was no hesitation as she threw herself forwards into the light. _"May you be in heaven half an hour before the Devil knows you're dead." _

The light hit her hands first, and it began to strip her bare of everything she was.

"_Not sure if Turian heaven is the same as yours, but if this thing goes sideways and we both end up there…meet me at the bar. I'm buying." _Shepard couldn't breathe.

God she loved him. If there was one thing she ever did right…it was loving Garrus Vakarian. The light was everywhere…it was everything…she was everything.

Shepard lost herself in a wash of light.


	4. Chapter 4

It was bright. Shepard frowned to herself and groaned, it wasn't just bright it was white. Shepard remembered old earth tales of there being a white light when a person died but this was just ridiculous. A land of entirely white light was a bit too much if you asked her. Shepard slowly tried to stand up and groaned some more.

She was still injured. Shepard briefly glanced at her arms and sighed. Still covered in blood. She honestly had thought that the after death would be a bit better than this. Shepard glanced around and froze when she came face to face with…herself.

But….not herself?

It was obviously her face, other than the Cerberus scars had never healed. But her eyes were a glowing blue. And she really did mean glowing blue. Not to mention the black hair instead of her normal blood red hair. The armor was different too…and she was pretty sure that she wasn't making that exact expression.

"I'm Commander Shepard, Alliance Navy. Who are you?" The black-haired Shepard asked looking startled.

"I'm…Commander Shepard. What's going on here?"


End file.
